Structural Chemogenomics Group
Laboratoire d'Innovation Therapeutique, UMR7200 CNRS/Universite de Strasbourg
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Software
| Name | Language | Description |
|---|---|---|
| SpaceDock | Python | A structure-based method to screen ultra-large chemical spaces |
| ProCare | Python | A point cloud registration approach to align protein cavities |
| IChem 5.2.9 | C++ | A toolkit to detect, analyze and compare protein-ligand interactions License key upon request to Dr. Didier Rognan (rognan[@]unistra.fr) |
| Shaper2 | C++ | Update of the Shaper method for Shape-based alignment of pharmacophore-annotated VolSite cavities (Version 2) |
| Shaper | C++ | Shape-based alignment of pharmacophore-annotated VolSite cavities (Version 1) |
| SiteAlign 4.0 | C | A simple and fuzzy method to align and compare druggable protein binding sites (Schalon et al., Proteins, 2008) Licence file upon request to Dr. Didier Rognan (rognan[@]unistra.fr) |
| FuzCav | Java | A novel alignment-free high-throughput algorithm to compute pairwise similarities between protein_ligand binding sites ( Weill et al. , J Chem Info Model, 2010 ) |
| FingerPrintLib | C++ | Computes molecular interaction fingerprints (Marcou et al. J Chem Info Model, 2007 ) |
| pymolFP | Python | Interaction fingerprints viewer integrated in a pymol plugin |
| Fresno | C++ | Empirical scoring function (Rognan et al. J Med Chem, 1999 ) |
Datasets
| File | Description |
|---|---|
| PDBbind dataset | In-house curated input files (protein, ligand) of the PDBbind v.2019 dataset. |
| LIT-PCBA dataset | LIT-PCBA: A dataset for virtual screening and machine learning Tran-Nguyen et al. J Chem Inf Model, 60, 4263-4273, 2020 |
| PPIome dataset | Druggable cavities/Ligands at and nearby protein-protein interfaces from the Protein Data Bank da Silva et al. J Med Chem, 60, 4263-4273, 2019 |
| Fragdock dataset | 2376 ligand/protein structures aligned describing 64 different proteins. |
| Input/Output files for detecting PPIs and related cavities | Input/Output files for detetecting PPIs and related cavities |
| PDBBind Test set | PDBbind Test Set: 195 protein-ligand complexes (curated mol2 files). Gabel et al. J Chem Inf Model, 54, 2807-2815, 2014 |
| Mod-PDBbind | Set of decoy poses (0-5 Ang. rmsd to X-ray) for the 195 PDBbind test ligands Gabel et al. J Chem Inf Model, 54, 2807-2815, 2014 |
| DUD-E docking poses | Protein, ligand and docked poses for 10 DUD-E activity classes Gabel et al. J Chem Inf Model, 54, 2807-2815, 2014 |
| Docking.tar.gz | Docking dataset: 100 input files (protein, active site, ligand) from Kellenberger and al. Protein, 2004 |
| Screening.zip | Virtual screening datasets: Input files for receptor and ligand database (10 actives + 990 decoys) for both the tymidine kinase and the estrogen receptor alpha from Bissantz and al., J Med Chem, 2000 |
Miscellaneous tools
| Name | Language | Description |
|---|---|---|
| bestGoldScorer | Java | Recover the best or all GOLD poses according yours requirements. |
| marvinEditButton | PHP | Marvin edit button extension is a mediawiki extension to draw compounds in Mediawiki. |